mskcc / smile-server

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SMILE clinical importer - relax certain restrictions preventing samples from getting imported #1324

Open ao508 opened 2 hours ago

ao508 commented 2 hours ago
  1. Relax restriction on tumor sequencing date parsing (not always available in CVR JSON)
  2. Relax restriction on only allow samples to get imported if their corresponding DMP patient ID maps to a CMO ID in the CRDB crosswalk table

Stack trace #1

java.text.ParseException: Unparseable date: ""
    at java.base/java.text.DateFormat.parse(DateFormat.java:395) ~[na:na]
    at org.mskcc.smile.service.util.SampleDataFactory.resolveDmpCollectionYear(SampleDataFactory.java:192) ~[service-0.1.0.jar!/:0.1.0]
    at org.mskcc.smile.service.util.SampleDataFactory.buildNewSampleMetadataFromDmpSample(SampleDataFactory.java:162) ~[service-0.1.0.jar!/:0.1.0]
    at org.mskcc.smile.service.util.SampleDataFactory.buildNewClinicalSampleFromMetadata(SampleDataFactory.java:106) ~[service-0.1.0.jar!/:0.1.0]
    at org.mskcc.smile.service.impl.ClinicalMessageHandlingServiceImpl$1.onMessage(ClinicalMessageHandlingServiceImpl.java:252) ~[service-0.1.0.jar!/:0.1.0]
    at org.mskcc.cmo.messaging.impl.JSGatewayImpl.onMessage(JSGatewayImpl.java:234) ~[smile-messaging-java-1.4.1.RELEASE.jar!/:1.0.0-SNAPSHOT]
    at org.mskcc.cmo.messaging.impl.JSGatewayImpl.lambda$subscribe$0(JSGatewayImpl.java:198) ~[smile-messaging-java-1.4.1.RELEASE.jar!/:1.0.0-SNAPSHOT]
    at io.nats.client.impl.NatsDispatcher.run(NatsDispatcher.java:98) ~[jnats-2.10.0.jar!/:2.10.0]
    at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) ~[na:na]
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) ~[na:na]
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) ~[na:na]
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) ~[na:na]
    at java.base/java.lang.Thread.run(Thread.java:829) ~[na:na]
ao508 commented 1 hour ago

Please add your planning poker estimate with Zenhub @qu8n